github for collaboration (in RStudio)

github & science

The need for a logical way to organize and control revisions has existed for almost as long as writing has existed, but revision control became much more important, and complicated, when the era of computing began.

version control

• long been used to maintain code repositories in the software industry.
  • especially in open source software.
• science increasingly computational.
  • demands for increased openness.

http://billmills.github.io/scienceXpython/

modern science workflows

can be overwhelming

succesful modern science workflows

can be extremely powerful

github for science

ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts.

Rstudio for r users

invest in next generation science skills

…or get left behind

repos

centralising information e.g. ROpenSci / rfishbase

issues

project management

commits

project tracking

commits

traceability

entire process of project evolution reproducible

start with a repo

fork it

• make your own copy of the repository on github
• fork are linked and traceable

clone: copy repo link

• use link to pull down a local copy
• manage process through projects in Rstudio

create new project

• checkout from github
• defaults to gthub repo name

make a change

• open params_tmpl.R
• save as new .R in params/ folder.

commit

• make small commits often
• write informative messages

push

• push changes up to github

create pull request

• create request to merge fork to master

your mission

• fork the repo
• link it up to an Rstudio project
• create a new file params .R script. Name it using your initials (use 3 to be safe)
• enter parameters for your species.

ß

$(function () { // on page load replace all src URLs

$('.animated-gif').each(function (i, e) {
    disableGif(e)
});

}); Reveal.addEventListener(‘slidechanged’, initAnimatedGifs); Reveal.addEventListener(‘ready’, initAnimatedGifs);

function initAnimatedGifs(event) { $(‘.animated-gif’, event.currentSlide).each(function (i, e) { enableGif(e) });

if (event.previousSlide)
    $('.animated-gif', event.previousSlide).each(function (i, e) {
        disableGif(e)

    });

}

function enableGif(e) { var src = $(e).attr(“src”) $(e).attr(‘src’, src.replace(‘-image.gif’, ‘.gif’));

} function disableGif(e) { var src = $(e).attr(“src”) $(e).attr(‘src’, src.replace(‘.gif’, ‘-image.gif’));

}